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Series GSE226097 Query DataSets for GSE226097
Status Public on Mar 25, 2023
Title A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ.
Overall design Using a standardized nucleus extraction method, single-nucleus RNA seq was performed on whole Arabidopsis organs and tissues, including seeds, seedlings, rosettes, stems, flowers, and siliques, at ten developmental timepoints throughout the entire lifecycle of the plant. A minimum of four single-nucleus RNA-seq runs were performed per tissue and timepoint.
Contributor(s) Lee TA, Nobori T, Illouz-Eliaz N, Jow B, Nery JR, Ecker JR
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Submission date Feb 24, 2023
Last update date Mar 25, 2023
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL26208 Illumina NovaSeq 6000 (Arabidopsis thaliana)
Samples (84)
GSM7063664 0-day-old imbibed seeds, run 1, snRNA-seq
GSM7063665 0-day-old imbibed seeds, run 2, snRNA-seq
GSM7063666 0-day-old imbibed seeds, run 3, snRNA-seq
BioProject PRJNA938501
SRA SRP424479

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE226097_221121_curio_seed_seurat.rds.gz 222.8 Mb (ftp)(http) RDS
GSE226097_flower_230221.rds.gz 251.8 Mb (ftp)(http) RDS
GSE226097_rosette_21d_230221.rds.gz 582.6 Mb (ftp)(http) RDS
GSE226097_rosette_30d_230221.rds.gz 890.3 Mb (ftp)(http) RDS
GSE226097_seed_0d_230221.rds.gz 308.7 Mb (ftp)(http) RDS
GSE226097_seed_125d_230221.rds.gz 15.8 Gb (ftp)(http) RDS
GSE226097_seedling_12d_230221.rds.gz 2.1 Gb (ftp)(http) RDS
GSE226097_seedling_3d_230221.rds.gz 255.6 Mb (ftp)(http) RDS
GSE226097_seedling_6d_230221.rds.gz 1.2 Gb (ftp)(http) RDS
GSE226097_silique_230221.rds.gz 2.0 Gb (ftp)(http) RDS
GSE226097_stem_230221.rds.gz 430.4 Mb (ftp)(http) RDS
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